my own board

I made an arduino board myself.

But i did not upload the bootloader into it because i am planing to use ponyprog and write my own programs. Can i do this?

Well the web page says it supports a Atmega 168 so assuming that is what you used I don't see why it would not work. However, in that case it is not an Arduino you have but just an embedded processor.

The thing that makes an embedded process an Arduino is the boot loader and the support libraries and C extensions.